Wastewater Surviellence for SARS-CoV-2 in Athens, GA
Lipp Laboratory, Department of Environmental Health Science, University of Georgia
2022-06-16
Load all required libraries.
library(tidyverse)## -- Attaching packages --------------------------------------- tidyverse 1.3.1 --## v ggplot2 3.3.5 v purrr 0.3.4
## v tibble 3.1.6 v dplyr 1.0.8
## v tidyr 1.2.0 v stringr 1.4.0
## v readr 2.1.2 v forcats 0.5.1## -- Conflicts ------------------------------------------ tidyverse_conflicts() --
## x dplyr::filter() masks stats::filter()
## x dplyr::lag() masks stats::lag()library(plotly)##
## Attaching package: 'plotly'## The following object is masked from 'package:ggplot2':
##
## last_plot## The following object is masked from 'package:stats':
##
## filter## The following object is masked from 'package:graphics':
##
## layoutlibrary(broom)Read in raw data from RDS.
raw_data <- readRDS("./n1_n2_cleaned_cases.rds")Make a few small modifications to names and data for visualizations.
final_data <- raw_data %>% mutate(log_copy_per_L = log10(mean_copy_num_L)) %>%
rename(Facility = wrf) %>%
mutate(Facility = recode(Facility,
"NO" = "WRF A",
"MI" = "WRF B",
"CC" = "WRF C"))Seperate the data by gene target to ease layering in the final plot
#make three data layers
only_positives <<- subset(final_data, (!is.na(final_data$Facility)))
only_n1 <- subset(only_positives, target == "N1")
only_n2 <- subset(only_positives, target == "N2")
only_background <<-final_data %>%
select(c(date, cases_cum_clarke, new_cases_clarke, X7_day_ave_clarke)) %>%
group_by(date) %>% summarise_if(is.numeric, mean)
#specify fun colors
background_color <- "#7570B3"
seven_day_ave_color <- "#E6AB02"
marker_colors <- c("N1" = '#1B9E77',"N2" ='#D95F02')#remove facilty C for now
#only_n1 <- only_n1[!(only_n1$Facility == "WRF C"),]
#only_n2 <- only_n2[!(only_n2$Facility == "WRF C"),]
only_n1 <- only_n1[!(only_n1$Facility == "WRF A" & only_n1$date == "2020-11-02"), ]
only_n2 <- only_n2[!(only_n2$Facility == "WRF A" & only_n2$date == "2020-11-02"), ]Build the main plot
#KEEP BOTH TARGETS HERE ON THE ALL DATA PLOT
#first layer is the background epidemic curve
p1 <- only_background %>%
plotly::plot_ly() %>%
plotly::add_trace(x = ~date, y = ~new_cases_clarke,
type = "bar",
hoverinfo = "text",
text = ~paste('</br> Date: ', date,
'</br> Daily Cases: ', new_cases_clarke),
alpha = 0.5,
name = "Daily Reported Cases",
color = background_color,
colors = background_color,
showlegend = FALSE) %>%
layout(yaxis = list(title = "Daily Cases", showline=TRUE)) %>%
layout(legend = list(orientation = "h", x = 0.2, y = -0.3))
#renders the main plot layer two as seven day moving average
p1 <- p1 %>% plotly::add_trace(x = ~date, y = ~X7_day_ave_clarke,
type = "scatter",
mode = "lines",
hoverinfo = "text",
text = ~paste('</br> Date: ', date,
'</br> Seven-Day Moving Average: ', X7_day_ave_clarke),
name = "Seven Day Moving Average Athens",
line = list(color = seven_day_ave_color),
showlegend = FALSE)
#renders the main plot layer three as positive target hits
p2 <- plotly::plot_ly() %>%
plotly::add_trace(x = ~date, y = ~mean_copy_num_L,
type = "scatter",
mode = "markers",
hoverinfo = "text",
text = ~paste('</br> Date: ', date,
'</br> Facility: ', Facility,
'</br> Target: ', target,
'</br> Copies/L: ', round(mean_copy_num_L, digits = 2)),
data = only_n1,
symbol = ~Facility,
marker = list(color = '#1B9E77', size = 8, opacity = 0.65),
showlegend = FALSE) %>%
plotly::add_trace(x = ~date, y = ~mean_copy_num_L,
type = "scatter",
mode = "markers",
hoverinfo = "text",
text = ~paste('</br> Date: ', date,
'</br> Facility: ', Facility,
'</br> Target: ', target,
'</br> Copies/L: ', round(mean_copy_num_L, digits = 2)),
data = only_n2,
symbol = ~Facility,
marker = list(color = '#D95F02', size = 8, opacity = 0.65),
showlegend = FALSE) %>%
layout(yaxis = list(title = "SARS CoV-2 Copies/L",
showline = TRUE,
type = "log",
dtick = 1,
automargin = TRUE)) %>%
layout(legend = list(orientation = "h", x = 0.2, y = -0.3))
#adds the limit of detection dashed line
p2 <- p2 %>% plotly::add_segments(x = as.Date("2020-03-14"),
xend = ~max(date + 10),
y = 3571.429, yend = 3571.429,
opacity = 0.35,
hoverinfo = "text",
text = "Limit of Detection",
line = list(color = "black", dash = "dash")) %>%
layout(annotations = list(x = as.Date("2020-03-28"), y = 3.8, xref = "x", yref = "y",
text = "Limit of Detection", showarrow = FALSE))
p1 p2Combine the two main plot pieces as a subplot
p_combined <-
plotly::subplot(p2,p1, # plots to combine, top to bottom
nrows = 2,
heights = c(.6,.4), # relative heights of the two plots
shareX = TRUE, # plots will share an X axis
titleY = TRUE
) %>%
# create a vertical "spike line" to compare data across 2 plots
plotly::layout(
xaxis = list(
spikethickness = 1,
spikedash = "dot",
spikecolor = "black",
spikemode = "across+marker",
spikesnap = "cursor"
),
yaxis = list(spikethickness = 0)
)
p_combinedSave the plot to pull into the index
save(p_combined, file = "./all_data.rda")rejoin <- readRDS("./rejoin.rds")Build loess smoothing figures figures
#create smoothing data frames
#n1
smooth_n1 <- only_n1 %>% select(-c(Facility)) %>%
group_by(date, cases_cum_clarke, new_cases_clarke, X7_day_ave_clarke) %>%
summarize(sum_copy_num_L = sum(mean_total_copies)) %>%
ungroup() %>%
mutate(log_sum_copies_L = log10(sum_copy_num_L)) %>%
mutate(target = "N1")## `summarise()` has grouped output by 'date', 'cases_cum_clarke',
## 'new_cases_clarke'. You can override using the `.groups` argument.#n2
smooth_n2 <- only_n2 %>% select(-c(Facility)) %>%
group_by(date, cases_cum_clarke, new_cases_clarke, X7_day_ave_clarke) %>%
summarize(sum_copy_num_L = sum(mean_total_copies)) %>%
ungroup() %>%
mutate(log_sum_copies_L = log10(sum_copy_num_L)) %>%
mutate(target = "N2")## `summarise()` has grouped output by 'date', 'cases_cum_clarke',
## 'new_cases_clarke'. You can override using the `.groups` argument.#add trendlines
#extract data from geom_smooth
#average targets extract
# *********************************span 0.6***********************************
#*****************Must always update the n = TOTAL NUMBER OF DAYS*************************
extract <- ggplot(rejoin, aes(x = date, y = log_sum_copies_both)) +
stat_smooth(aes(outfit=fit_both<<-..y..), method = "loess", color = '#1B9E77',
span = 0.25, n = 716)## Warning: Ignoring unknown aesthetics: outfit#look at the fits to align dates and total observations
#both
extract## `geom_smooth()` using formula 'y ~ x'
#assign fits to a vector
both_trend <- fit_both
#extract y min and max for each
limits_both <- ggplot_build(extract)$data## `geom_smooth()` using formula 'y ~ x'limits_both <- as.data.frame(limits_both)
both_ymin <- limits_both$ymin
both_ymax <- limits_both$ymax
#reassign dataframes (just to be safe)
work_both <- rejoin
#fill in missing dates to smooth fits
work_both <- work_both %>% complete(date = seq(min(date), max(date), by = "1 day"))
date_vec_both <- work_both$date
#create a new smooth dataframe to layer
smooth_frame_both <- data.frame(date_vec_both, both_trend, both_ymin, both_ymax)#make plotlys
#plot smooth frames
p3 <- plotly::plot_ly() %>%
plotly::add_lines(x = ~date_vec_both, y = ~both_trend,
data = smooth_frame_both,
hoverinfo = "text",
text = ~paste('</br> Date: ', date_vec_both,
'</br> Median Log Copies: ', round(both_trend, digits = 2)),
line = list(color = '#1B9E77', size = 8, opacity = 0.65),
showlegend = FALSE) %>%
plotly::add_ribbons(x ~date_vec_both, ymin = ~both_ymin, ymax = ~both_ymax,
showlegend = FALSE,
opacity = 0.25,
hoverinfo = "text",
text = ~paste('</br> Date: ', date_vec_both, #leaving in case we want to change
'</br> Max Log Copies: ', round(both_ymax, digits = 2),
'</br> Min Log Copies: ', round(both_ymin, digits = 2)),
name = "",
fillcolor = '#1B9E77',
line = list(color = '#1B9E77')) %>%
layout(yaxis = list(title = "Total Log10 SARS CoV-2 Copies",
showline = TRUE,
automargin = TRUE)) %>%
layout(xaxis = list(title = "Date")) %>%
plotly::add_segments(x = ~min(date_vec_both),
xend = ~max(date_vec_both),
y = 11.5, yend = 11.5,
opacity = 0.35,
name = "</br> Below Limit of Detection",
hoverinfo = "text",
text = "Below Limit of Detection",
showlegend = FALSE,
line = list(color = "black", dash = "dash")) %>%
plotly::add_annotations(x = as.Date("2021-02-15"),
y = 11.5,
text = "Limit of Detection") %>%
plotly::add_markers(x = ~date, y = ~log_sum_copies_both,
data = rejoin,
hoverinfo = "text",
showlegend = FALSE,
text = ~paste('</br> Date: ', date,
'</br> Actual Log Copies: ', round(log_sum_copies_both, digits = 2)),
marker = list(color = '#1B9E77', size = 6, opacity = 0.65))
p3Create final trend plot by stacking with epidemic curve
smooth_extract <-
plotly::subplot(p3,p1, # plots to combine, top to bottom
nrows = 2,
heights = c(.6,.4), # relative heights of the two plots
shareX = TRUE, # plots will share an X axis
titleY = TRUE
) %>%
# create a vertical "spike line" to compare data across 2 plots
plotly::layout(
xaxis = list(
spikethickness = 1,
spikedash = "dot",
spikecolor = "black",
spikemode = "across+marker",
spikesnap = "cursor"
),
yaxis = list(spikethickness = 0)
)
smooth_extractsave(smooth_extract, file = "./plotly_fig.rda")Save an htmlwidget for website embedding
htmlwidgets::saveWidget(smooth_extract, "plotly_fig.html")#six weeks ago
last_6 <- Sys.Date() - 42
#next filter base frames
filter_n1 <- filter(only_n1, date >= last_6)
filter_n2 <- filter(only_n2, date >= last_6)
filter_background <- filter(only_background, date >= last_6)
filter_smooth_frame_both <- filter(smooth_frame_both, date_vec_both >= last_6)
filter_rejoin <- filter(rejoin, date >= last_6) #first layer is the background epidemic curve
p1_filter <- filter_background %>%
plotly::plot_ly() %>%
plotly::add_trace(x = ~date, y = ~new_cases_clarke,
type = "bar",
hoverinfo = "text",
text = ~paste('</br> Date: ', date,
'</br> Daily Cases: ', new_cases_clarke),
alpha = 0.5,
name = "Daily Reported Cases",
color = background_color,
colors = background_color,
showlegend = FALSE) %>%
layout(yaxis = list(title = "Daily Cases", showline=TRUE)) %>%
layout(legend = list(orientation = "h", x = 0.2, y = -0.3))
#renders the main plot layer two as seven day moving average
p1_filter <- p1_filter %>% plotly::add_trace(x = ~date, y = ~X7_day_ave_clarke,
type = "scatter",
mode = "lines",
hoverinfo = "text",
text = ~paste('</br> Date: ', date,
'</br> Seven-Day Moving Average: ', X7_day_ave_clarke),
name = "Seven Day Moving Average Athens",
line = list(color = seven_day_ave_color),
showlegend = FALSE)
#renders the main plot layer three as positive target hits
p2_filter <- plotly::plot_ly() %>%
plotly::add_trace(x = ~date, y = ~mean_copy_num_L,
type = "scatter",
mode = "markers",
hoverinfo = "text",
text = ~paste('</br> Date: ', date,
'</br> Facility: ', Facility,
'</br> Target: ', target,
'</br> Copies/L: ', round(mean_copy_num_L, digits = 2)),
data = filter_n1,
symbol = ~Facility,
marker = list(color = '#1B9E77', size = 8, opacity = 0.65),
showlegend = FALSE) %>%
plotly::add_trace(x = ~date, y = ~mean_copy_num_L,
type = "scatter",
mode = "markers",
hoverinfo = "text",
text = ~paste('</br> Date: ', date,
'</br> Facility: ', Facility,
'</br> Target: ', target,
'</br> Copies/L: ', round(mean_copy_num_L, digits = 2)),
data = filter_n2,
symbol = ~Facility,
marker = list(color = '#D95F02', size = 8, opacity = 0.65),
showlegend = FALSE) %>%
layout(yaxis = list(title = "SARS CoV-2 Copies/L",
showline = TRUE,
type = "log",
dtick = 1,
automargin = TRUE)) %>%
layout(legend = list(orientation = "h", x = 0.2, y = -0.3))
#adds the limit of detection dashed line
p2_filter <- p2_filter %>% plotly::add_segments(x = as.Date(last_6),
xend = ~max(date + 10),
y = 3571.429, yend = 3571.429,
opacity = 0.35,
hoverinfo = "text",
text = "Limit of Detection",
line = list(color = "black", dash = "dash")) %>%
layout(annotations = list(x = as.Date(last_6), y = 3.8, xref = "x", yref = "y",
text = "Limit of Detection", showarrow = FALSE))
p1_filter p2_filterfilter_combined <-
plotly::subplot(p2_filter,p1_filter, # plots to combine, top to bottom
nrows = 2,
heights = c(.6,.4), # relative heights of the two plots
shareX = TRUE, # plots will share an X axis
titleY = TRUE
) %>%
# create a vertical "spike line" to compare data across 2 plots
plotly::layout(
xaxis = list(
spikethickness = 1,
spikedash = "dot",
spikecolor = "black",
spikemode = "across+marker",
spikesnap = "cursor"
),
yaxis = list(spikethickness = 0)
)
filter_combinedp3_filter <- plotly::plot_ly() %>%
plotly::add_trace(x = ~date, y = ~sum_copies_both,
type = 'scatter',
mode = 'lines+markers',
data = filter_rejoin,
hoverinfo = "text",
showlegend = FALSE,
text = ~paste('</br> Date: ', date,
'</br> SARS CoV-2 Copies: ', round(sum_copies_both, digits = 2)),
line = list(color = '#1B9E77', size = 6, opacity = 0.65),
marker = list(color = '#1B9E77', size = 8, opacity = 0.65)) %>%
layout(yaxis = list(title = "Total SARS CoV-2 Copies",
showline = TRUE,
automargin = TRUE)) %>%
plotly::add_segments(x = ~last_6,
xend = ~max(date_vec_both),
y = 11.5, yend = 11.5,
opacity = 0.35,
name = "</br> Below Limit of Detection",
hoverinfo = "text",
text = "Below Limit of Detection",
showlegend = FALSE,
line = list(color = "black", dash = "dash"))
#%>%
# plotly::add_annotations(x = as.Date(last_6 + 7),
# y = 11.5,
# text = "Limit of Detection")
p3_filtersmooth_extract_filter <-
plotly::subplot(p3_filter,p1_filter, # plots to combine, top to bottom
nrows = 2,
heights = c(.6,.4), # relative heights of the two plots
shareX = TRUE, # plots will share an X axis
titleY = TRUE
) %>%
# create a vertical "spike line" to compare data across 2 plots
plotly::layout(
xaxis = list(
spikethickness = 1,
spikedash = "dot",
spikecolor = "black",
spikemode = "across+marker",
spikesnap = "cursor"
),
yaxis = list(spikethickness = 0)
)
smooth_extract_filtersave(smooth_extract_filter, file = "./smooth_extract_filter.rda")